Immune Diversity

Team “Deaminases and lymphocyte fate determination”

Team leader: Dr. Elias Amro

Team members: Christos Gkougkousis, Nina Lemmen

Research Summary

Differentiation into specific cell fates and maintenance of cell identity require molecular programs driven by transcription factors that not only sustain cell-specific identities but also suppress alternative cell fates. Our recent research has focused on exploring the role of APOBEC2 in lymphoid lineage specification. APOBEC2 is part of the highly conserved apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like (APOBEC) family, known for its zinc-dependent deaminase activity (Pecori et al., 2022; Wedekind et al., 2003; Harris et al., 2002; Powell et al., 2014). While most members of this family catalyze the conversion of cytidine to uridine within DNA or RNA, resulting in C-to-U transitions, APOBEC2 lacks this enzymatic function. Despite this, APOBEC2 plays an unconventional role in regulating biological functions both in vitro and in vivo. In mice, depletion of Apobec2 leads to muscle weakness, reduced muscle mass, and a shift from fast to slow twitching muscle fiber formation (Sato et al., 2010; Mikl et al., 2005; Sato et al., 2018). Apobec2 has also been implicated in cancer development through mutations and altered gene expression (Okuyama et al., 2012; Wei et al., 2024; Li et al., 2019). Recent research from our lab (Lorenzo, Molla, Amro et al., 2024) has uncovered a novel role for APOBEC2 as a transcription factor that maintains muscle identity by suppressing non-muscle genes. Beyond muscle biology, our current work reveals that APOBEC2 deficiency in mice and humans causes defects in lymphoid lineage specification. Human individuals with homozygous APOBEC2 mutations show weakened immune responses to vaccination and have increased susceptibility to immune dysfunction (Amro, Gkougkousis et al., unpublished). To further unravel the role and function of APOBEC2 in health and disease, our team's research focuses on two main objectives:

• understanding the molecular mechanisms by which Apobec2 regulates lymphoid lineage specification;

• elucidating the impact of Apobec2 mutations on the human immune system functions.

Collaborations

• Dr. Charles Imbusch (Uni Mainz)
• Prof. Dr. Christoph Dieterich (Uni Heidelberg)
• Prof. Dr. Lennart Hammarström (Karolinska Institutet)
• Prof. Dr. Qian Pan Hammarström (Karolinska Institutet)
• Prof. Dr. Fowzan AlKuraya (King Faisal Hospital, Riyadh)

Publications

• Lorenzo, Molla, Amro, et al. APOBEC2 safeguards skeletal muscle cell fate through binding chromatin and regulating transcription of non-muscle genes during myoblast differentiation. Proceedings of the National Academy of Science, 2024.
• Pecori, et al. Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination. Nature Reviews Genetics, 2022.

Team “T. brucei derived tools: NanoVAST”

Team leader: Dr. Katerina Spyridopoulou

Team members: Laura Pezzella, Niklas Veocic

Research Summary

Targeted delivery of therapeutic agents to specific cell types remains a significant challenge in advancing fields such as gene therapy, RNA modification, and drug delivery. While technologies like CRISPR/Cas hold immense therapeutic potential, their clinical translation is hampered primarily by the lack of safe, efficient, and targeted delivery systems. Current delivery approaches, including electroporation and viral vectors, suffer from limitations like toxicity and immunogenicity.

To address this, our team utilizes nanoVAST, a novel platform developed by our colleagues at Panosome GmbH. NanoVAST comprises a patented vesicular phospholipid bilayer based on scalable production of African trypanosome-derived extracellular nanovesicles. Being biogenic, nanoVAST does not exhibit toxicity, while its fusogenic properties enable cytoplasmic delivery of its cargo. Critically, it is highly targetable, as its surface can be modified using a specific sortase-based chemistry – termed VAST – to attach targeting moieties.

We are optimizing nanoVAST for in vitro, ex vivo, and in vivo therapeutic cargo delivery, exploring its biochemical properties to develop highly specific cell-targeting strategies. Our work focuses on the development of cargo-specific loading methodologies and cell-specific targeting approaches for cancer and immune cells (such as T cells and NK cells). Cargo types that are currently being investigated include TCR-mRNA, CAR mRNA, siRNA, guide RNAs for RNA editing, and DNA vectors. We also develop and employ state-of-the-art technologies to assess optimized nanoVAST production, cargo loading, and effective and functional cellular delivery.

By improving the targeted delivery of drugs and gene therapy systems, this technology has the potential to unlock new therapeutic avenues for numerous diseases currently lacking effective treatments.

Grants

• European Research Council 2022 Proof of Concept Grant (nanoVAST)
• DKFZ seed funding program 2024: Kick-start DreamTeam Grant

Collaborations

• Prof. Dr. med. Michael Platten (DKFZ)
• Prof. Dr. Joachim Spatz (MPI for Medical Research)
• Synthetic Immunology Research Network

Publications

• Hempelmann, et al. Nanobody-mediated macromolecular crowding induces membrane fission and remodeling in the African trypanosome. Cell Reports, 2021.

Team “T. brucei derived tools: VAST and the development of antibodies as therapeutics”

Team leader: Dr. Joseph (Joey) Peter Verdi

Team members: Dr. Monica Chandra, Dr. Anastasia Gkeka, Dr. Nataliia Kashpur, Eblina Kelmendi, Seneca Kinn-Gurzo, Dr. Jose Paulo Lorenzo, Dr. Colin Miller, Eleftheria Papamanoglu, Sandra Ruf, Dr. Eirini Sidiropoulou

Research Summary

Keytruda, Humira, Herceptin… Many human diseases can now be treated successfully with antibody-based therapies. Our team aims to expand the repertoire of antibody-treatable diseases using our internally developed technology platform for antibody generation. While it has now become relatively simplistic to generate high-quality antibodies against protein antigens, there remains a general inability to reproducibly generate the same quality of antibodies against small molecules and carbohydrates. These notably small-sized molecules are associated with or the cause of just as many diseases as proteins are, yet this space has yet to be convincingly explored. Here, we do exactly that - we specifically chase after these “difficult targets” with the intention of developing novel therapies.

To attack these difficult targets, we developed a platform technology based on the unique surface architecture of the African trypanosome. The surface of Trypanosoma brucei cells is extremely densely packed with 10 million copies of one protein - the variant surface glycoprotein (VSG). This uniquely dense and uniformly oriented array of antigens stimulates the immune system in a remarkable way, directing virtually the entire disease-relevant antibody response towards epitopes localised on just the very top of the VSG protein. This so-called “epitope focusing” effect is perhaps the strongest of its kind in nature, which our team has harnessed by “sortagging” (fusing) these difficult targets to the surface of VSG and creating the VSG Immunogen Array by Sortase Tagging - the VAST. As examples of the VAST’s applicability, the technology has so far been used to make a series of pico- and femtomolar affinity antibodies to the opioids fentanyl and carfentanil that can completely prevent opioid toxicity in animal model systems, as well as a series of high-quality antibodies to carbohydrates present on mucin 1 (MUC1), a high-priority target in solid tumor cancers. This exciting technology, its antibody products, and every exceptionally talented member of this team form the cornerstone of a biotechnology start-up company, Panosome GmbH, located in the local Heidelberg area. 

Grants

• 2024, KMU-innovativ (BMBF) project “CarboVAST” awarded to Panosome GmbH with DKFZ as a collaborating institution (Dr. Verdi and Prof. Papavasiliou as project leaders)
• 2024, KMU-innovativ (BMBF) project “GliomAb” awarded to Panosome GmbH with DKFZ as a collaborating institution (Dr. Verdi and Prof. Papavasiliou as project leaders).
• European Research Council 2020 Proof of Concept Grant (EpiMODkit)

Collaborations

• Prof. Dr. Rienk Offringa (DKFZ)
• Prof. Dr. med. Michael Platten (DKFZ)
• Dr. Aubry Miller (DKFZ)
• Dr. Erec Stebbins (DKFZ)

Selected Publications

• Urban and Gkeka et al., The fentanyl-specific antibody FenAb024 can shield against carfentanil effects. Toxicology Letters, 2024.
• Triller et al., A trypanosome-derived immunotherapeutics platform elicits potent high-affinity antibodies, negating the effects of the synthetic opioid fentanyl. Cell Reports, 2023.
• Gkeka and Aresta-Branco et al., Immunodominant surface epitopes power immune evasion in the African trypanosome. Cell Reports, 2023.
• Triller et al., Immunization with Genetically Modified Trypanosomes Provides Protection against Transmissible Spongiform Encephalopathies. International Journal of Molecular Sciences, 2022.